The problem is that ISPConfig might have created some configuration files in the one docroot and some others in the other docroot.
Never cahnge anything in the database directly, use always the ISPConfig interface!
To get a clean version of the config tree again, you should delete all websites, wait about 1 - 2 minutes, then empty the recycle bin. Then make sure your docroot setting in ISPConfig under management > server > settings is correct and create the websites and email users again.
You dont have to delete the resellers and clients as thei do not have any configuration inside the document root tree.